I've been fiddling with my 2000 Honda Civic LX for a few weeks and I cannot seem to pinpoint the problem. I have researched and ruled out the brake booster as the culprit. Well here's the problem.
*With the car off, the pedal feels firm and seems like it's working. It builds and keeps pressure because I stepped and held the pedal 80% for approximately 30 seconds and it did not lose pressure. So I'm guessing that there are no leaks in the system. Now with the car ON, the pedal softens due to the brake booster, and the brakes start engaging when the pedal is down 80% of the way. The pedal feels too soft and engages late. The fluid level in the reservoir seems to stay at the same level. The pedal does come back up, it just engages late. I have bled the system 4 times, twice with the 1-man bleeder, and twice with an assistant.
*What I have checked:
Both Front Calipers: No sign of fluid/leak.
Both Rear Drums: Pulled cover off and no sign of fluid/leak.
Brake Pads on all 4 corners: Good
Lines connecting to Master Cylinder and Calipers there are NO leaks/signs of fluid.
*What I did: I replaced the Master Cylinder twice from 2 different Honda Civics. The Master Cylinder is used because my friend works at the salvage yard and hooked me up with those. So I'm asking, is there a high possibility to have my master cylinder, and 2 others go bad? Or is there another problem?

So what can be the problem? I'm thinking about buying a rebuilt Master Cylinder from O'reillys tomorrow, but I'm afraid that it won't be the problem. Is there a way that my calipers can have an "internal" leak without showing any signs of a fluid leak? I apologize for making this so long but I would like to include as much information as I can. Thank you in advance!

 

Don't do any of that, simply adjust the rear brake drums, odds are your parking brake sucks, or engages very high provided you haven't fiddled with the parking brake adjustment under the console.

If that doesn't work (it will, I do this for a living), bleed the brakes to rule out air. Since your convinced it is the master cylinder at fault, I know the hydraulic system has been opened to replace it.

What happened to the car to make it have a low pedal?

 

Wow, I cannot thank you enough! I should have posted on here earlier instead of spend weeks trying to solve this problem. After reading and trusting in your response, I ran outside at 1:05AM, threw the car in neutral and tested the e-brake. I was excited to find out how loose it was lol and tightened where it starts engaging in 2+ clicks. After that, I started the car and was stunned at how much improvement it had caused in the pedal response! Though it was improvement, I would like the pedal to feel a tad bit stiffer. Where/how should I go about adjusting the rear brake drums to improve the braking response? I'm sure that there is an alternative way to adjust it besides the center console. Also, can you please explain to me why adjusting the e-brake cable would improve the response of the braking system? I have an idea but a thorough explanation would greatly improve my knowledge in cars and assist me in the future. Thank you very much for your professionalism! You solved my problem!!

*I will also continue my research and further understand the hydraulic braking system in my car. I must understand before fixing!

Oh and I purchased the car for $800. It was missing a radiator, catalytic converter, had a blown ignition fuse and the braking problem. After finding and replacing the blown fuse, the car fired right up! Later that week, I searched on Craigslist for a TIG welder and welded on a catalytic converter I had in the shed. Radiator ran me $24 from Ebay and now I'm just getting the car ready for emissions and registration!

 

DO NOT adjust the parking brake adjuster until you have adjusted the rear brake shoes, that is the source of your low pedal. THe parking brake adjuster should only be adjusted if when the rear brakes are in complete adjustment, the parking brake still engages high, indicating the cables have stretched and require tightening.

All you did was press the parking brake side of the brakes up against the brake drum, which may overheat the brake drums, and lead to one shoe wearing significantly faster than the other.